Contacts of the helix formed by residues 408 - 416 (chain A) in PDB entry 1R4N
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 408 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396A ARG* 3.7 30.3 - - - +
401A GLU* 5.2 0.4 + - - +
406A THR 2.9 6.8 + - - -
407A ILE* 1.3 69.8 - - - +
409A LYS* 1.3 56.5 + - - +
410A ASP* 3.2 7.7 + - - +
411A GLU* 2.9 35.6 + - - +
412A ILE* 3.7 12.8 + - - +
533A GLN* 4.1 25.9 + - - +
534A LEU* 5.4 3.8 - - - +
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Residues in contact with LYS 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404A LEU 5.8 1.2 + - - -
407A ILE* 2.4 43.8 + - + +
408A ASN* 1.3 65.3 - - - +
410A ASP* 1.3 66.0 + - - +
412A ILE* 3.9 6.0 - - - +
413A ILE* 3.3 29.9 + - + +
468A TYR 3.5 25.4 + - - +
469A GLY* 3.7 15.9 + - - +
470A LEU* 3.4 18.8 - - + -
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Residues in contact with ASP 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408A ASN* 3.2 6.8 - - - +
409A LYS* 1.3 81.4 - - - +
411A GLU* 1.3 59.0 + - - +
413A ILE* 3.9 2.9 - - - +
414A SER* 2.9 33.5 + - - -
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Residues in contact with GLU 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408A ASN* 2.9 23.8 + - - +
410A ASP* 1.3 78.4 - - - +
412A ILE* 1.3 65.9 + - + +
414A SER* 4.0 10.8 + - - -
415A SER* 3.1 38.4 + - - -
423A ILE* 6.3 0.4 - - + -
532A PHE* 4.1 15.9 - - + -
533A GLN* 3.6 36.8 + - + +
534A LEU 4.6 1.6 + - - -
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Residues in contact with ILE 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407A ILE* 3.5 28.3 - - + -
408A ASN 3.7 11.6 + - - +
409A LYS* 4.1 6.3 - - - +
410A ASP 3.3 0.6 - - - -
411A GLU* 1.3 80.3 - - + +
413A ILE* 1.3 65.5 + - + +
415A SER* 3.3 3.1 + - - -
416A MET* 3.1 31.5 + - + +
423A ILE* 4.5 21.2 - - + +
426A TYR* 4.8 13.9 - - + -
427A LEU* 4.1 26.9 - - + -
464A PHE* 5.7 1.6 - - + -
470A LEU* 4.0 24.0 - - + -
472A VAL* 5.1 3.4 - - + -
533A GLN* 5.4 7.0 - - - +
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Residues in contact with ILE 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409A LYS* 3.3 22.0 - - + +
410A ASP* 3.4 4.1 + - - +
411A GLU 3.4 0.2 - - - -
412A ILE* 1.3 71.9 - - - +
414A SER* 1.3 67.5 + - - +
415A SER 3.1 0.9 + - - -
416A MET* 3.1 14.4 + - + +
417A ASP* 3.6 13.9 + - - +
469A GLY 5.3 2.5 - - - +
470A LEU* 4.2 17.9 - - + -
471A SER* 4.5 23.1 - - - +
472A VAL* 4.1 25.6 - - + -
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Residues in contact with SER 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410A ASP* 2.9 22.2 + - - -
411A GLU* 3.5 17.0 + - - -
412A ILE 3.3 0.2 - - - -
413A ILE* 1.3 78.1 - - - +
415A SER* 1.3 57.9 + - - +
417A ASP* 2.5 26.1 + - - +
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Residues in contact with SER 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411A GLU* 3.1 26.4 + - - -
412A ILE 3.7 3.8 - - - -
414A SER* 1.3 73.6 - - - +
416A MET* 1.3 53.3 + - - +
417A ASP* 2.5 20.3 + - - +
418A ASN* 3.4 8.8 + - - +
421A ASN* 3.9 28.8 + - - +
423A ILE* 3.8 19.5 - - - -
532A PHE* 3.8 14.9 - - - -
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Residues in contact with MET 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412A ILE* 3.1 15.4 + - + +
413A ILE* 3.1 11.7 + - + +
415A SER* 1.3 73.5 - - - +
417A ASP* 1.3 55.3 + - - +
418A ASN* 2.9 19.8 + - - +
419A PRO* 4.0 9.6 - - + +
423A ILE* 3.3 23.8 - - + -
424A VAL* 4.0 23.6 - - + -
427A LEU* 3.8 27.4 - - + -
472A VAL* 3.8 29.6 - - + -
473A MET 3.7 26.4 + - - +
474A VAL* 4.2 11.4 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il